Peak Calling with 'MOSAiCS'

R package 'mosaics' implements MOSAiCS, a statistical framework for the analysis of ChIP-seq data, proposed in

Kuan PF, Chung D, Pan G, Thomson JA, Stewart R, and Keles S (2010).
“A Statistical Framework for the Analysis of ChIP-Seq Data.” (Submitted)

MOSAiCS stands for “MOdel-based one and two Sample Analysis and Inference for ChIP-Seq Data”.
Based on careful investigation of biases in ChIP-seq data such as mappability and GC content,
MOSAiCS has been developed as a fexible mixture modeling approach for detecting
peaks of one-sample (ChIP sample) or two-sample (ChIP sample and matched control sample) ChIP-seq data.


Installing MOSAiCS

If you are using windows,

You can obtain windows binary here.
Run your R console and install R package by selecting in your menu

Package > Install package(s) from local zip files...

and choose the windows binary you downloaded (mosaics_0.0.9.zip).

For linux & mac (possibly including windows, if necessary),

You can obtain R package source here.
Save it to the directory you prefer and install it by the following command.

> R CMD INSTALL mosaics_0.0.9.tar.gz


Using MOSAiCS

The incorporated R package vignette provides easy-to-follow guidelines.

If you have any questions regarding R package,
please post your question at google group for R package 'mosaics'
or e-mail Dongjun Chung at chungdon_at_stat_dot_wisc_dot_edu.